Crowds of joyful Libyans, some with tears in their eyes, parted with the legacy of Moamar Gaddafi's dictatorship on Saturday as they voted in the first free national election in more than 50 years.

But in the eastern city of Benghazi, the cradle of last year's uprising where many now want more autonomy from the interim government in Tripoli, protesters stormed a handful of polling stations and publicly burned hundreds of ballot papers.

Authorities also reported a case of gunmen preventing voters from entering polling stations in the eastern oil port town of Ras Lanuf, but said 94 per cent of polling stations around the North African country were up and running normally.

Libyans are choosing a 200-member assembly which will elect a prime minister and cabinet before laying the ground for full parliamentary elections next year under a new constitution.

Polls close at early on Sunday morning (AEST) but meaningful partial results are not due until Sunday and a full preliminary count is not expected until Monday at the earliest.

Candidates with Islamic agendas dominate the field of more than 3,700 hopefuls, suggesting Libya will be the next Arab Spring country - after Egypt and Tunisia - to see religious parties secure a grip on power.

In Benghazi, protesters stormed a polling station just after voting started and set fire to hundreds of ballot slips in a public square in a bid to undermine the election's credibility.

Witnesses said at least four polling stations had been hit in such attacks. One man was shot in the arm and taken to hospital with heavy bleeding after a stand-off between vote boycotters and those in favour of the elections.

"There wasn't enough security at the station to stop the attackers," said Nasser Zwela, adding protesters armed with assault rifles had stormed one local polling station and shouted at everyone to stop voting.

Yet in the capital Tripoli, voting was smooth. Loud religious cries went up inside one polling station as voting began in a converted school building abuzz with the chatter of queuing locals.

"I am a Libyan citizen in free Libya," said Mahmud Mohammed Al-Bizamti. "I came today to be able to vote in a democratic way. Today is like a wedding for us."

Some voters struggled with procedures for casting their ballot. In one central Tripoli district, two women disappeared into a voting booth together before an election worker hurriedly explained they must vote alone.

"Some of these women are crying as they vote. It is such an emotional day," said one poll official.

More autonomy

There is growing unrest in parts of Libya with armed groups in eastern Libya shutting off half the North African country's oil exports to press demands for more autonomy ahead of the vote.

A helicopter carrying voting material made a forced landing near the eastern town of Benghazi on Friday (local time) after being struck by anti-aircraft fire in an attack which killed one person on board, local officials said.

"We were preparing to receive the voting material as it arrived on a helicopter from Tripoli but it was hit and one man died," Ahmed Abdelmalik, an employee at the local branch of the election commission, said.

The election for a temporary national assembly comes barely a year after former dictator Moamar Gaddafi was ousted in a NATO-backed uprising.

But a spate of attacks on election facilities in the east and calls for a vote boycott there show how regional loyalties suppressed under Gaddafi have come to the fore in a country where armed militias dominate under-resourced security forces.

"There is no security in this country," High National Election Commission deputy head Emad El-Sayih said.

"The interior ministry and the army are incapable of protecting the elections. The (election) commission is in a state of depression."

On Thursday, the main storage centre for election materials in the eastern town of Ajdabiya was badly damaged in a suspected arson attack and last weekend armed men stormed the local election office in Benghazi and destroyed equipment.

'Civil war' possible

In a concession to the easterners, the interim government on Thursday announced the panel which will write the new constitution will be elected directly by Libyans in another election.

Easterners are angry their region, one of three in Libya, has only been allocated 60 of the 200 seats in the new assembly compared to 102 in the west around the capital Tripoli - a formula the interim government says is based on their weighting within a national population of six million.

"There is no doubt there could be a civil war between us in the east and the west because we do not have an equal number of seats as the west," Hamed al-Hassi, head of the High Military Council of Cyrenaica, the name of the eastern region, said.

"The country will be in a state of paralysis because no one in the government is listening to us."

Shippers said half Libya's oil exporting capacity had been shut down and production cut by about 300,000 barrels per day because of protests by groups demanding greater autonomy in the east, home to the bulk of its reserves.

At least three major oil exporting terminals were closed Thursday evening and by Friday the first delays to oil shipments were reported by oil traders waiting for cargoes to load.

Oil companies hoping to lift shipments of crude from the ports affected by the shutdown received a note from agents warning vessels would not be able to berth or load while the strike continued.

"The strikes will continue for 48 hours if the government does not respond positively to their requests," the note said.